Taxon Constraint for His-Purkinje system in fish

[michaelerice]

Request review for taxon constraint for HIs-Purkinje GO terms
GO:0060933
GO:0060934
GO:0060933
GO:0003168
GO:0086054
GO:0086055
GO:0086028
GO:0086073
GO:0086078
never_in_taxon Actinopterygii 7898, Coelacanthiformes 7894, Dipnoi 7878

PMID: 12626327 PMID: 21234997

Thank you
GOC:MR

[tberardini]

You want to add these constraints, correct?

[michaelerice]

?Yes Tanya,

Thank you

---

Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Sciences
Thomas W. Keating Bioresearch Building
1657 E. Helen St.
Tucson, AZ 85721
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu

---

From: Tanya Berardini notifications@github.com
Sent: Thursday, May 19, 2016 6:03 PM
To: geneontology/go-ontology
Cc: Rice, Michael E - (mrice); Author
Subject: Re: [geneontology/go-ontology] Taxon Constraint for His-Purkinje system in fish (#12451)

You want to add these constraints, correct?

You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHubhttps://github.com//issues/12451#issuecomment-220492323

[tberardini]

Your list:

• GO:0060933, His-Purkinje system cell development
• GO:0060934, His-Purkinje system cell fate commitment
• GO:0060932, His-Purkinje system cell differentiation
• GO:0003168, Purkinje myocyte differentiation
• GO:0086054, bundle of His cell to Purkinje myocyte communication by electrical coupling
• GO:0086055, Purkinje myocyte to ventricular cardiac muscle cell communication by electrical coupling
• GO:0086028, bundle of His cell to Purkinje myocyte signaling
• GO:0086073, bundle of His cell-Purkinje myocyte adhesion involved in cell communication
• GO:0086078, gap junction channel activity involved in bundle of His cell-Purkinje myocyte electrical coupling

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What about GO:0003164, His-Purkinje system development ? There are 34 terms that contain the word 'Purkinje', 20 that contain 'bundle of His'. Do you mean to add the taxon restrictions to all of these (some will inherit the restriction by parentage) or just the specific subset that you put in your original request?

[michaelerice]

Tanya,

all of the terms containing His and Purkinje should be covered by the restriction. sorry, when I saw how many there are I did not finish the list thinking it would be covered by the review process. Thanks for working on this.

Mike

---

Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Sciences
Thomas W. Keating Bioresearch Building
1657 E. Helen St.
Tucson, AZ 85721
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu

---

From: Tanya Berardini notifications@github.com
Sent: Friday, May 20, 2016 9:29 AM
To: geneontology/go-ontology
Cc: Rice, Michael E - (mrice); Author
Subject: Re: [geneontology/go-ontology] Taxon Constraint for His-Purkinje system in fish (#12451)

Your list:

• GO:0060933, His-Purkinje system cell development
• GO:0060934, His-Purkinje system cell fate commitment
• GO:0060932, His-Purkinje system cell differentiation
• GO:0003168, Purkinje myocyte differentiation
• GO:0086054, bundle of His cell to Purkinje myocyte communication by electrical coupling
• GO:0086055, Purkinje myocyte to ventricular cardiac muscle cell communication by electrical coupling
• GO:0086028, bundle of His cell to Purkinje myocyte signaling
• GO:0086073, bundle of His cell-Purkinje myocyte adhesion involved in cell communication
• GO:0086078, gap junction channel activity involved in bundle of His cell-Purkinje myocyte electrical coupling

---

What about GO:0003164, His-Purkinje system development ? There are 34 terms that contain the word 'Purkinje', 20 that contain 'bundle of His'. Do you mean to add the taxon restrictions to all of these (some will inherit the restriction by parentage) or just the specific subset that you put in your original request?

You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHubhttps://github.com//issues/12451#issuecomment-220654022

[tberardini]

Hi Mike - With the giant number of open Github tickets and the relatively small amount of ontology editors' time, the best chance for getting things done quickly is to provide as much detail in the request as possible. :) Thanks for the clarification.

[michaelerice]

?

ok, thanks

sorry for the incompleteness.

---

Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Sciences
Thomas W. Keating Bioresearch Building
1657 E. Helen St.
Tucson, AZ 85721
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu

---

From: Tanya Berardini notifications@github.com
Sent: Friday, May 20, 2016 9:54 AM
To: geneontology/go-ontology
Cc: Rice, Michael E - (mrice); Author
Subject: Re: [geneontology/go-ontology] Taxon Constraint for His-Purkinje system in fish (#12451)

Hi Mike - With the giant number of open Github tickets and the relatively small amount of ontology editors' time, the best chance for getting things done quickly is to provide as much detail in the request as possible. :) Thanks for the clarification.

You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHubhttps://github.com//issues/12451#issuecomment-220659813

[tberardini]

Looked into this issue a little further:

1. We need to import Coelacanthiformes 7894, Dipnoi 7878 into taxa used for GO.
2. It's probably cleaner to place the restriction on the UBERON terms instead and have the related GO terms inherit those taxon restrictions.

@michaelerice: Can you figure out which terms in UBERON are the most appropriate to restrict to the taxa that you requested?

Here's a search I did for His-Purkinje using AmiGO

http://amigo.geneontology.org/amigo/search/ontology?q=his-purkinje&fq=source:%22uberon%22&sfq=document_category:%22ontology_class%22

I was thinking this one:

http://amigo.geneontology.org/amigo/term/UBERON:0004146

@cmungall - you might be interested in this ticket

blocked on #12223

[cmungall]

I am very interested

We have grouped the teleost (and thus Actinopterygii) distal conduction system in with His-Purkinje system

The evidence may have been weak. E.g. ZFA uses "His-Purkinji network" as an exact syn. This was an early merge in uberon

What is the relationship between these structures? Haven't had time to read the references.

Summoning homology and comparative fish anatomy people: @ANiknejad @mellybelly @ybradford @cerivs

[cmungall]

Ah OK, so the original ZFA entry was a mistake, it has been obsoleted:

[Term]
id: ZFA:0005071
name: distal conduction system
namespace: zebrafish_anatomy
is_obsolete: true
consider: ZFA:0005059  ! trabecular layer
comment: Appears to be mammalian due to exact synonym His-Perkinje system, which doesn't have an exact analog in fish (or frogs). PMID:22984480 PLoS One. 2012;7(9):e44231.
synonym: "HPS" EXACT []
synonym: "His-Purkinje system" EXACT []
synonym: "His-Purkinji network" EXACT []
xref: TAO:0005071

From a skim of the refs it seems that lower vertebrates have a functional analog but is histologically different; the functional analog is the trabecular layer

[cmungall]

OK, I think the representation of the analogous tissue in uberon has a lot of gaps I'd like to fill, but we should take that over to the uberon tracker

For now I will add the required TC, and we'll call this ticket closed

btw, I am going be bold and rewrite the TC as only-in tetrapoda (the 3 negative constraints as originally stated leaves open the possibility of the HPS being in Chondrichthyes, or even in cyclostomes, but this seems biologically unlikely based on the 3 papers here)